We developed a whole genome sequencing assay for coxsackievirus A24 variant (CA24v), a major cause of acute hemorrhagic conjunctivitis, and used it to recover three near complete genomes from the 2024 CA24v outbreak in Kenya. This assay will support studies on CA24v genomic epidemiology and evolution across Africa. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement Funding for this work is from a Wellcome (grant no. 226002/A/22/Z), The Rockefeller Foundation (Grant OXF-FDG01), and National Institute of Health and Care Research (grant. NIHR156467). ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: This study/analysis was reviewed and approved by KEMRI Scientific Ethics Review Unit (SERU) Committee based in Nairobi, Kenya (Protocol #: KEMRI/SERU/CGMR-C/304/4894). I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes The genome sequences reported in this work are available in GenBank under accessions [PQ683184][1] - [PQ683186][2]. The raw sequencing reads are available in NCBI Sequence Read Archive (SRA) under BioProject accession PRJNA1193512. [1]: /lookup/external-ref?link_type=GEN&access_num=PQ683184&atom=%2Fmedrxiv%2Fearly%2F2025%2F01%2F16%2F2025.01.16.25320645.atom [2]: /lookup/external-ref?link_type=GEN&access_num=PQ683186&atom=%2Fmedrxiv%2Fearly%2F2025%2F01%2F16%2F2025.01.16.25320645.atom

Background: Understanding the molecular epidemiology and clinical presentation of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOC) in rural-urban populations in Kenya is important for informing future public health responses and clinical care. Methods: We undertook a retrospective analysis of the clinical presentation and phylogenetic relatedness of specimens from 97 SARS-CoV-2 cases collected between 24th April and 31st December 2021 in Laikipia county, Kenya. VOC were related to observed symptoms. Phylogenetic analyses included contemporaneous sequences from across Kenya and the globe, to contextualise local transmission dynamics. Results: These sequences fell into three VOC; Alpha (n=8), Delta (n=52) and Omicron (n=37). We estimated 75 independent SARS-CoV-2 introductions into the county. The Alpha and Delta VOC were commonly detected in persons aged 31 to 45 years, 50.0% and 30.8%, respectively. The Omicron VOC was mostly detected in 16 to 30-year-olds (51.4%). Whereas relative to the other VOCs, Omicron was associated with mild upper-respiratory tract symptoms (cough, OR 3.78; 95% CI 1.1 – 16.74, p= 0.026) and sore throat, OR 22.42; 95% CI 7.11 – 81.40, p<0.001), Delta was associated with moderate to severe lower-respiratory tract symptoms (shortness of breath, OR 26.8; 95% CI 3.89 – 1158.14, p<0.001) and fever (OR 6.11; 95% CI 1.57 – 35.35, p= 0.004). Post-acute phase neurological complications were suspected in four Delta infected cases (neuralgia, neuritis, peripheral neuropathy, numbness of hand and tinnitus). Conclusion: We highlight the distinctive clinical characteristics of SARS-CoV-2 VOCs, as observed in Laikipia, Kenya, to support evidence-based clinical decisions. Multiple introductions of the VOCs were recorded despite the public health measures that were in place questioning their effectiveness during the study period.

Background In early 2024, a surge in acute hemorrhagic conjunctivitis (AHC), also referred as “red eye” disease, was observed in coastal Kenya, prompting the Ministry of Health to issue an outbreak alert. Herein, we investigated the etiology of this outbreak. Methods Ocular swabs were obtained from 13 individuals presenting with AHC at a Mombasa clinic in early February 2024. Ten of these were analyzed using bacterial cultures, and all 13 using a pan-adenovirus quantitative PCR (qPCR) and metagenomic sequencing. Potential viral etiology was confirmed by a specific qPCR, amplicon sequencing and phylogenetic analysis. Results Bacterial cultures yielded no growth except in three samples where non-pathogenic bacteria were detected. All 13 samples were adenovirus qPCR negative. Metagenomic sequencing detected coxsackievirus A24 variant (CA24v) in three of the 13 samples. CV-A24v detections were confirmed by both CV-A24v specific qPCR and amplicon sequencing of an approximately 450 nucleotide long VP4/2 junction genomic region. Phylogenetic analysis of the VP4/2 sequences showed that they were closely related to CV-A24v genotype IV. Conclusion The AHC epidemic in coastal Kenya in early 2024 was likely caused by CA24v. Metagenomic sequencing is a powerful tool for identifying potential causative agents of new disease outbreaks.

Background In early 2024, a surge in acute hemorrhagic conjunctivitis (AHC), also referred as “red eye” disease, was observed in coastal Kenya, prompting the Ministry of Health to issue an outbreak alert. Herein, we investigated the etiology of this outbreak. Methods Ocular swabs were obtained from 13 individuals presenting with AHC at a Mombasa clinic in early February 2024. Ten of these were analyzed using bacterial cultures, and all 13 using a pan-adenovirus quantitative PCR (qPCR) and metagenomic sequencing. Potential viral etiology was confirmed by a specific qPCR, amplicon sequencing and phylogenetic analysis. Results Bacterial cultures yielded no growth except in three samples where non-pathogenic bacteria were detected. All 13 samples were adenovirus qPCR negative. Metagenomic sequencing detected coxsackievirus A24 variant (CA24v) in three of the 13 samples. CV-A24v detections were confirmed by both CV-A24v specific qPCR and amplicon sequencing of an approximately 450 nucleotide long VP4/2 junction genomic region. Phylogenetic analysis of the VP4/2 sequences showed that they were closely related to CV-A24v genotype IV. Conclusion The AHC epidemic in coastal Kenya in early 2024 was likely caused by CA24v. Metagenomic sequencing is a powerful tool for identifying potential causative agents of new disease outbreaks.

The recombinant FY.4 SARS-CoV-2 variant was first reported in Kenya in March 2023 and was the dominant circulating variant between April and July 2023. The variant was characterised by two important mutations: Y451H in the receptor binding domain of the spike protein and P42L in open reading frame 3a. Using phylogenetics and phylodynamic approaches, we investigated the emergence and spread of the FY.4 in Kenya and the rest of the world. Our findings suggest FY.4 circulated early in Kenya before export to North America and Europe. Early circulation of FY.4 in Kenya was predominantly observed in the coastal part of the country and the estimated time to the most recent common ancestor suggests FY.4 circulated as early as December 2022. The collected genomic and epidemiological data show that the FY.4 variant led to a large local outbreak in Kenya and resulted in localised outbreaks in Europe, North America and Asia-pacific. These findings underscore the importance of sustained genomic surveillance especially in under sampled regions in deepening our understanding of the evolution and spread of SARS-CoV-2 variants. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement This work was support by multiple funding sources that included the New Variant Assessment Platform (NVAP), Wellcome grants (220985/Z/20/Z and 226002/A/22/Z). The Rockerfeller Foundation subaward (OXFFDG01) and the Department of Health and Social Care grant (project references 17/63/82 and 16/136/33). The views expressed in this publication are those of the author (s) and not necessarily those of the Department of Health and Social Care, Foreign Commonwealth and Development Office, Wellcome Trust or the UK government ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The whole genome sequencing study protocol was reviewed and approved by the Scientific and Ethics Review Committee (SERU) residing at the Kenya Medical Research Institute (KEMRI) headquarters in Nairobi (SERU # 4035). I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes All data produced in the present work are contained in the manuscript

AbstractA multi-pronged approach to combating the COVID-19 pandemic in Kenya resulted in the formation of multidisciplinary research initiatives including genomic sequencing, syndromic surveillance, sero-surveillance, vaccination, and mathematical modelling. These initiatives generated an overwhelming amount of data that posed a challenge to researchers and public health officials, to effectively manage, analyse and promptly interpret for immediate pandemic response. As a result, there was demand for a platform to collate and integrate these datasets with interpretable findings to aid in pandemic management. In response, we developed a web-based dashboard, and integrated multidisciplinary datasets collected by the Ministry of Health-Kenya (MoH-K) and other research organizations, to support surveillance and monitoring of COVID-19 in Kenya. The developed dashboard combines genomics, epidemiological, seroprevalence, modelling, vaccination, syndromic and phylogenetic data and provides real-time updates to the public and health sector experts. The dashboard provides temporal trends of reported COVID-19 cases, fatalities, variants, and vaccination, in addition to summary reports from multiple cross-sectional seroprevalence studies and ongoing facility-based inpatient syndromic surveillance from 15 health facilities across Kenya. This is the first detailed interactive dashboard in Kenya that combines multiple datasets from a disease outbreak to provide valuable insights to researchers, health policy makers, the media and public not only during pandemic but also during routine surveillance. This resource is a model for digital platform for infectious disease surveillance and for informing public health planning and intervention.Dashboard Linkhttps://kcd.kemri-wellcome.org/

Continuous genomic surveillance is necessary and important to inform emergence of new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants and resurgence of previous circulating variants. In this study, we provide genomic characterisation of a Beta variant sequence identified through out genomic surveillance platform more than a year since the last reported case of Beta. This variant contained additional mutations associated with immune escape that have been observed in other newer variants such as Delta and Omicron implying ongoing convergent evolution of this variant in the community or in an immunocompromised patient.

SARS-CoV-2 was first detected in Sudan on 13 th March 2020. Here, we describe the genomic epidemiology of SARS-CoV-2 in Sudan between May 2020 and April 2022 to understand the introduction and transmission of SARS-CoV-2 variants in the country. A total of 667 SARS-CoV-2 positive samples were successfully sequenced using the nCoV-19 Artic protocol on the Oxford Nanopore Technology (≥70% genome completeness). The genomes were compared with a select contemporaneous global dataset to determine genetic relatedness and estimate import/export events. The genomes were classified into 37 Pango lineages within the ancestral strain (107 isolates across 13 Pango lineages), Eta variant of interest (VOI) (78 isolates in 1 lineage), Alpha variant of concern (VOC) (10 isolates in 2 lineages), Beta VOC (26 isolates in 1 lineage), Delta VOC (171 isolates across 8 lineages) and Omicron VOC (242 isolates across 12 lineages). We estimated a total of 144 introductions of the observed variants from different countries across the globe. Multiple introductions of the Eta VOI, Beta VOC and Omicron VOC were observed in Sudan mainly from Europe and Africa. These findings suggest a need for continuous genomic surveillance of SARS-CoV-2 to monitor their introduction and spread consequently inform public health measures to combat SARS-CoV-2 transmission.

We report a newly emerged SARS-CoV-2 Omicron sub variant FY.4 that has mutations Y451H in spike and P42L in open reading frame 3a proteins. FY.4 emergence coincided with increased SARS-CoV-2 cases in coastal Kenya during April-May 2023. Continued SARS-CoV-2 genomic surveillance is needed to identify new lineages to inform COVID-19 outbreak prevention.

We report a newly emerged SARS-CoV-2 Omicron lineage, named FY.4, that has two unique mutations; spike:Y451H and ORF3a:P42L. FY.4 emergence has coincided with increased SARS-CoV-2 cases in coastal Kenya, April-May 2023. We demonstrate the value of continued SARS-CoV-2 genomic surveillance in the post-acute pandemic era in understanding new COVID-19 outbreaks.

We report emergence and predominance of the influenza A (H3N2) subclade 3C.2a1b.2a.2a.3a.1 in Kenya similar to the global clade in 2023. The Kenyan 3C.2a1b.2a.2a.3a.1 viruses have >15 amino acid differences in the HA and NA proteins relative to 2023/24 WHO recommended Northern/Southern Hemisphere influenza vaccine strains. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement This work was supported by The Wellcome, UK (grant nos. 226002/A/22/Z and 220985/Z/20/Z), New Variant Assessment Programme, a UK Health Security Agency program funded by the UK Department of Health and Social Care as a global initiative to strengthen genomic surveillance for pandemic preparedness and response to emerging and priority infectious diseases; the UK National Institute for Health and Care Research (project references 17/63/82 and 16/136/33) that uses aid from the UK government to support global health research; UK Foreign, Commonwealth and Development Office. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: Ethical approval for the study protocol was obtained from the Scientific and Ethics Review Unit (SERU number 1858) ethics committee, Kenya Medical Research Institute, Nairobi, Kenya. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes All data generated and analysis script for this manuscript are available from the Virus Epidemiology and Control, Kenya Medical Research Institute (KEMRI)Wellcome Trust Research Programme data server:https://doi.org/10.7910/DVN/5US8MM, Full-length viral genomes are available in GISAID EpiFlu (accession nos EPI\_ISL\_18560856 - EPI\_ISL\_18560859 and EPI\_ISL\_18560907 - EPI\_ISL\_18560947)

Background: The emergence of the Omicron variant of concern in late 2021 led to a resurgence of SARS-CoV-2 infections globally. By September 2022, Seychelles had experienced two major surges of SARS-CoV-2 infections driven by the Omicron variant. Here, we examine the genomic epidemiology of Omicron in the Seychelles between November 2021 and September 2022. Methods: We analysed 618 SARS-CoV-2 Omicron genomes identified in the Seychelles between November 2021 and September 2022 to infer virus introductions and local transmission patterns using phylogenetics and the ancestral state reconstruction approach. We then evaluated the impact of government coronavirus 2019 (COVID-19) countermeasures on the estimated number of viral introductions during the study period. Results: The genomes classified into 43 distinct Pango lineages. The first surge in Omicron cases (beginning November 2021 and peaking in January 2022) was predominated by the BA.1.1 lineage (59%) co-circulating with 11 other Omicron lineages. In the second surge (between April and June 2022), four lineages (BA.2, BA.2.10, BA.2.65 and BA.2.9) co-circulated and these were swiftly replaced by BA.5 subvariants in July 2022, which remained predominant through to September 2022. In the latter period, sporadic detections of BA.5 subvariants BQ.1, BE and BF were observed. We estimated 109 independent Omicron importations into Seychelles over the 11-month period, most of which occurred between December 2021 and March 2022 when strict government restrictions (SI>50%) were still in force. The districts Anse Royale, and Baie St. Anne Praslin appeared to be the major dispersal points fuelling local transmission. Conclusions: Our results suggest that the waves of Omicron infections in the Seychelles were driven by multiple lineages and multiple virus introductions. The introductions were followed by substantial local spread and successive lineage displacement that mirrored the global patterns.

Introduction The ARTIC Network's primer set and amplicon-based protocol is one of the most widely used SARS-CoV-2 sequencing protocol. An update to the V3 primer set was released on 18th June 2021 to address amplicon drop-off observed among the Delta variant of concern. Here, we report on an in-house optimization of a modified version of the ARTIC Network V4 protocol that improves SARS-CoV-2 genome recovery in instances where the original V4 pooling strategy was characterized by amplicon drop-offs. Methods We utilized a matched set of 43 clinical samples and serially diluted positive controls that were amplified by ARTIC V3, V4 and optimized V4 primers and sequenced using GridION from the Oxford Nanopore Technologies'. Results We observed a 0.5% to 46% increase in genome recovery in 67% of the samples when using the original V4 pooling strategy compared to the V3 primers. Amplicon drop-offs at primer positions 23 and 90 were observed for all variants and positive controls. When using the optimized protocol, we observed a 60% improvement in genome recovery across all samples and an increase in the average depth in amplicon 23 and 90. Consequently, ≥95% of the genome was recovered in 72% (n = 31) of the samples. However, only 60–70% of the genomes could be recovered in samples that had <28% genome coverage with the ARTIC V3 primers. There was no statistically significant (p > 0.05) correlation between Ct value and genome recovery. Conclusion Utilizing the ARTIC V4 primers, while increasing the primer concentrations for amplicons with drop-offs or low average read-depth, greatly improves genome recovery of Alpha, Beta, Delta, Eta and non-VOC/non-VOI SARS-CoV-2 variants.

Seychelles, an archipelago of 155 islands in the Indian Ocean, had confirmed 24,788 cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by the 31st of December 2021. The first SARS-CoV-2 cases in Seychelles were reported on the 14th of March 2020, but cases remained low until January 2021, when a surge was observed. Here, we investigated the potential drivers of the surge by genomic analysis of 1056 SARS-CoV-2 positive samples collected in Seychelles between 14 March 2020 and 31 December 2021. The Seychelles genomes were classified into 32 Pango lineages, 1042 of which fell within four variants of concern, i.e., Alpha, Beta, Delta and Omicron. Sporadic cases of SARS-CoV-2 detected in Seychelles in 2020 were mainly of lineage B.1 (lineage predominantly observed in Europe) but this lineage was rapidly replaced by Beta variant starting January 2021, and which was also subsequently replaced by the Delta variant in May 2021 that dominated till November 2021 when Omicron cases were identified. Using the ancestral state reconstruction approach, we estimated that at least 78 independent SARS-CoV-2 introduction events occurred in Seychelles during the study period. The majority of viral introductions into Seychelles occurred in 2021, despite substantial COVID-19 restrictions in place during this period. We conclude that the surge of SARS-CoV-2 cases in Seychelles in January 2021 was primarily due to the introduction of more transmissible SARS-CoV-2 variants into the islands.